CHORD: Category-level Hand-held Object Reconstruction via Shape Deformation

In daily life, humans utilize hands to manipulate objects. Modeling the shape of objects that are manipulated by the hand is essential for AI to comprehend daily tasks and to learn manipulation skills. However, previous approaches have encountered difficulties in reconstructing the precise shapes of hand-held objects, primarily owing to a deficiency in prior shape knowledge and inadequate data for training. As illustrated, given a particular type of tool, such as a mug, despite its infinite variations in shape and appearance, humans have a limited number of 'effective' modes and poses for its manipulation. This can be attributed to the fact that humans have mastered the shape prior of the 'mug' category, and can quickly establish the corresponding relations between different mug instances and the prior, such as where the rim and handle are located. In light of this, we propose a new method, CHORD, for Category-level Hand-held Object Reconstruction via shape Deformation. CHORD deforms a categorical shape prior for reconstructing the intra-class objects. To ensure accurate reconstruction, we empower CHORD with three types of awareness: appearance, shape, and interacting pose. In addition, we have constructed a new dataset, COMIC, of category-level hand-object interaction. COMIC contains a rich array of object instances, materials, hand interactions, and viewing directions. Extensive evaluation shows that CHORD outperforms state-of-the-art approaches in both quantitative and qualitative measures. Code, model, and datasets are available at https://kailinli.github.io/CHORD.Comment: To be presented at ICCV 2023, Pari

Induced cultivation pattern enhanced the phycoerythrin production in red alga Porphyridium purpureum.

Porphyridium purpureum is a rich source for producing phycoerythrin (PE); however, the PE content is greatly affected by culture conditions. Researchers have aimed to optimize the cultivation of P. purpureum for accumulation of PE. When traditional optimized culture conditions were used to cultivate P. purpureum, high PE contents were not usually achieved. In this study, an induced cultivation pattern was applied to P. purpureum for PE biosynthesis (i.e., an incremental approach by altering temperatures, light intensities, and nitrate concentrations). Results revealed that the induced pattern greatly improved the PE biosynthesis. The optimized PE content of 229 mg/L was achieved on the 12th cultivation day, which was a maximum PE content within one cultivation period and accounted for approximately 3.05% of the dry biomass. The induced cultivation pattern was highly suitable for PE synthesis in P. purpureum, which provided an important reference value to the large-scale production of PE

Genome-wide identification and expression analysis of TCP family genes in Catharanthus roseus

IntroductionThe anti-tumor vindoline and catharanthine alkaloids are naturally existed in Catharanthus roseus (C. roseus), an ornamental plant in many tropical countries. Plant-specific TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors play important roles in various plant developmental processes. However, the roles of C. roseus TCPs (CrTCPs) in terpenoid indole alkaloid (TIA) biosynthesis are largely unknown.MethodsHere, a total of 15 CrTCP genes were identified in the newly updated C. roseus genome and were grouped into three major classes (P-type, C-type and CYC/TB1).ResultsGene structure and protein motif analyses showed that CrTCPs have diverse intron-exon patterns and protein motif distributions. A number of stress responsive cis-elements were identified in promoter regions of CrTCPs. Expression analysis showed that three CrTCP genes (CrTCP2, CrTCP4, and CrTCP7) were expressed specifically in leaves and four CrTCP genes (CrTCP13, CrTCP8, CrTCP6, and CrTCP10) were expressed specifically in flowers. HPLC analysis showed that the contents of three classic TIAs, vindoline, catharanthine and ajmalicine, were significantly increased by ultraviolet-B (UV-B) and methyl jasmonate (MeJA) in leaves. By analyzing the expression patterns under UV-B radiation and MeJA application with qRT-PCR, a number of CrTCP and TIA biosynthesis-related genes were identified to be responsive to UV-B and MeJA treatments. Interestingly, two TCP binding elements (GGNCCCAC and GTGGNCCC) were identified in several TIA biosynthesis-related genes, suggesting that they were potential target genes of CrTCPs. DiscussionThese results suggest that CrTCPs are involved in the regulation of the biosynthesis of TIAs, and provide a basis for further functional identification of CrTCPs

Analysis of Global Sea Level Change Based on Multi-Source Data

Global sea level rise is both a major indicator and consequence of global warming. At present, global warming is causing sea level rise in two main ways: one is the thermal expansion of sea water, and the other is the injection of large amounts of fresh water into the ocean after glaciers and ice sheets melt. In this paper, satellite altimeter data are used to study the total changes of global sea level from 2002 to 2020. Different from most previous studies, this study proposes a calculation method of sea level anomaly using only the along track altimetry data, which is similar to considering the satellite points as tide gauges, in order to avoid the error caused by interpolation in the map data. In addition, GRACE satellite data are used to calculate the changes of global sea level caused by water increase; temperature and salinity data are used to calculate the changes from ocean thermal expansion. Next, using satellite altimetry data, the calculation results show that the global sea level rise rate in the period of 2002–2020 is 3.3 mm/a. During this period, the sea level change caused by the increase of sea water calculated with GRACE satellite data is 2.07 mm/a, and that caused by the thermal expansion of seawater is 0.62 mm/a. The sea level rise caused by the increase of water volume accounts for 62.7% of the total sea level rise

Analysis of Global Sea Level Change Based on Multi-Source Data

Global sea level rise is both a major indicator and consequence of global warming. At present, global warming is causing sea level rise in two main ways: one is the thermal expansion of sea water, and the other is the injection of large amounts of fresh water into the ocean after glaciers and ice sheets melt. In this paper, satellite altimeter data are used to study the total changes of global sea level from 2002 to 2020. Different from most previous studies, this study proposes a calculation method of sea level anomaly using only the along track altimetry data, which is similar to considering the satellite points as tide gauges, in order to avoid the error caused by interpolation in the map data. In addition, GRACE satellite data are used to calculate the changes of global sea level caused by water increase; temperature and salinity data are used to calculate the changes from ocean thermal expansion. Next, using satellite altimetry data, the calculation results show that the global sea level rise rate in the period of 2002–2020 is 3.3 mm/a. During this period, the sea level change caused by the increase of sea water calculated with GRACE satellite data is 2.07 mm/a, and that caused by the thermal expansion of seawater is 0.62 mm/a. The sea level rise caused by the increase of water volume accounts for 62.7% of the total sea level rise

LC-MS/MS for Assessing the Incorporation and Repair of N2-Alkyl-2-deoxyguanosine in Genomic DNA.

Understanding the occurrence, repair, and biological consequences of DNA damage is important in environmental toxicology and risk assessment. The most common way to assess DNA damage elicited by exogenous sources in a laboratory setting is to expose cells or experimental animals with chemicals that modify DNA. Owing to the lack of reaction specificities of DNA damaging agents, the approach frequently does not allow for induction of a specific DNA lesion. Herein, we employed metabolic labeling to selectively incorporate N2-methyl-dG (N2-MedG) and N2-n-butyl-dG (N2-nBudG) into genomic DNA of cultured mammalian cells, and investigated how the levels of the two lesions in cellular DNA are modulated by different DNA repair factors. Our results revealed that nucleotide excision repair (NER) exert moderate effects on the removal of N2-MedG and N2-nBudG from genomic DNA. We also observed that DNA polymerases κ and η contribute to the incorporation of N2-MedG into genomic DNA and modulate its repair in human cells. In addition, loss of ALKBH3 resulted in higher frequencies of N2-MedG and N2-nBuG incorporation into genomic DNA, suggesting a role of oxidative dealkylation in the reversal of these lesions. Together, our study provided new insights into the repair of minor-groove N2-alkyl-dG lesions in mammalian cells

Proteome-wide Interrogation of Small GTPases Regulated by N6-Methyladenosine Modulators.

N6-Methyladenosine (m6A) in messenger RNA (mRNA) regulates its stability, splicing, and translation efficiency. Here, we explored how the expression levels of small GTPase proteins are regulated by m6A modulators. We employed a high-throughput scheduled multiple-reaction monitoring (MRM)-based targeted proteomic approach to quantify systemically the changes in expression of small GTPase proteins in cells upon genetic ablation of METTL3 (the catalytic subunit of the major m6A methyltransferase complex), m6A demethylases (ALKBH5 and FTO), or m6A reader proteins (YTHDF1, YTHDF2, and YTHDF3). Depletions of METTL3 and ALKBH5 resulted in substantially diminished and augmented expression, respectively, of a subset of small GTPase proteins, including RHOB and RHOC. Our results also revealed that the stability of RHOB mRNA is significantly increased in cells depleted of METTL3, suggesting an m6A-elicited destabilization of this mRNA. Those small GTPases that are targeted by METTL3 and/or ALKBH5 also displayed higher discrepancies between protein and mRNA expression in paired primary/metastatic melanoma or colorectal cancer cells than those that are not. Together, this is the first comprehensive analysis of the alterations in small GTPase proteome regulated by epitranscriptomic modulators of m6A, and our study suggests the potential of an alternative therapeutic approach to target the currently undruggable small GTPases

Biodegradation of Fumonisins by the Consecutive Action of a Fusion Enzyme

Fumonisins (FBs) are toxic mycotoxins that commonly exist in food and feed. FBs can induce many aspects of toxicity, leading to adverse effects on human and animal health; therefore, investigating methods to reduce fumonisin contamination is necessary. In our study, we generated a recombinant fusion enzyme called FUMDI by linking the carboxylesterase gene (fumD) and the aminotransferase gene (fumI) by overlapping polymerase chain reaction (PCR). The fusion enzyme FUMDI was successfully, secretively expressed in the host Pichia pastoris (P. pastoris) GS115, and its expression was optimized. Our results demonstrated that the fusion enzyme FUMDI had high biodegradation activity of fumonisin B1 (FB1) and other common FBs, such as fumonisin B2 (FB2) and fumonisin B3 (FB3), and almost completely degraded 5 μg/mL of each toxin within 24 h. We also found that FUMDI enzyme and its reaction products had no negative effect on cell viability and did not induce cell apoptosis, oxidative stress, or endoplasmic reticulum (ER) stress in a human gastric epithelial cell line (GES-1). The results indicated that these FBs degradation products cannot have adverse effects in a cell model. In conclusion, a safe and efficient fumonisin-degrading enzyme was discovered, which could be a new a technical method for hazard control of FBs in the future

Biodegradation of Fumonisins by the Consecutive Action of a Fusion Enzyme

Fumonisins (FBs) are toxic mycotoxins that commonly exist in food and feed. FBs can induce many aspects of toxicity, leading to adverse effects on human and animal health; therefore, investigating methods to reduce fumonisin contamination is necessary. In our study, we generated a recombinant fusion enzyme called FUMDI by linking the carboxylesterase gene (fumD) and the aminotransferase gene (fumI) by overlapping polymerase chain reaction (PCR). The fusion enzyme FUMDI was successfully, secretively expressed in the host Pichia pastoris (P. pastoris) GS115, and its expression was optimized. Our results demonstrated that the fusion enzyme FUMDI had high biodegradation activity of fumonisin B1 (FB1) and other common FBs, such as fumonisin B2 (FB2) and fumonisin B3 (FB3), and almost completely degraded 5 μg/mL of each toxin within 24 h. We also found that FUMDI enzyme and its reaction products had no negative effect on cell viability and did not induce cell apoptosis, oxidative stress, or endoplasmic reticulum (ER) stress in a human gastric epithelial cell line (GES-1). The results indicated that these FBs degradation products cannot have adverse effects in a cell model. In conclusion, a safe and efficient fumonisin-degrading enzyme was discovered, which could be a new a technical method for hazard control of FBs in the future